RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zft4j8/RM_26336.SatJul61026072024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1720286766 Database = /dev/shm/rModeler.zft4j8/GCF_000972845.2_L_crocea_2.0 - Sequences = 9998 - Bases = 657939657 - N50 = 29365971 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 48622334-52095323 | [ 2 ] 45149346-48622334 | [ ] 41676358-45149346 | [ 1 ] 38203370-41676358 | [ 1 ] 34730382-38203370 | [ ] 31257394-34730382 | [ 2 ] 27784406-31257394 | [ 2 ] 24311417-27784405 | [ 1 ] 20838429-24311417 | [ 7 ] 17365441-20838429 | [ 2 ] 13892453-17365441 | [ 2 ] 10419465-13892453 | [ 2 ] 6946477-10419465 | [ ] 3473489-6946477 | [ 2 ] 501-3473489 |************************************************** [ 9974 ] Storage Throughput = excellent ( 1029.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40145365 bp ( 40035369 non ambiguous ) - Num Contigs Represented = 702 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:27 (hh:mm:ss) Elapsed Time Round Time: 00:25:01 (hh:mm:ss) Elapsed Time : 383 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6416 repeats masked totaling 812309 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10055918 bp Num Contigs Represented = 197 Non ambiguous bp: Initial: 10028424 bp After Masking: 8917084 bp Masked: 11.08 % -- Input Database Coverage: 10055918 bp out of 657939657 bp ( 1.53 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 81810 Comparison Time: 00:06:50 (hh:mm:ss) Elapsed Time, 12262 HSPs Collected Number of families returned by RECON: 1667 Round Time: 00:07:59 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20909 repeats masked totaling 2753971 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30089367 bp Num Contigs Represented = 535 Non ambiguous bp: Initial: 30006865 bp After Masking: 26405345 bp Masked: 12.00 % -- Input Database Coverage: 40145285 bp out of 657939657 bp ( 6.10 % ) Sampling Time: 00:02:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 737505 Comparison Time: 00:37:58 (hh:mm:ss) Elapsed Time, 47508 HSPs Collected Number of families returned by RECON: 6082 Round Time: 00:42:56 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 72552 repeats masked totaling 9837775 bp(s). - TE Masking time 00:01:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90316307 bp Num Contigs Represented = 1439 Non ambiguous bp: Initial: 90023656 bp After Masking: 77869098 bp Masked: 13.50 % -- Input Database Coverage: 130461592 bp out of 657939657 bp ( 19.83 % ) Sampling Time: 00:07:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 6338580 Comparison Time: 04:35:20 (hh:mm:ss) Elapsed Time, 302214 HSPs Collected Number of families returned by RECON: 22926 Round Time: 05:00:50 (hh:mm:ss) Elapsed Time : 408 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 277873 repeats masked totaling 40402926 bp(s). - TE Masking time 00:08:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271040530 bp Num Contigs Represented = 4190 Non ambiguous bp: Initial: 270038224 bp After Masking: 222944663 bp Masked: 17.44 % -- Input Database Coverage: 401502122 bp out of 657939657 bp ( 61.02 % ) Sampling Time: 00:26:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 56908446 Comparison Time: 36:00:52 (hh:mm:ss) Elapsed Time, 994823 HSPs Collected Number of families returned by RECON: 90173 Round Time: 39:50:31 (hh:mm:ss) Elapsed Time : 1196 families discovered. RepeatScout/RECON discovery complete: 2100 families found Classification Time: 01:32:40 (hh:mm:ss) Elapsed Time Program Time: 47:39:58 (hh:mm:ss) Elapsed Time